ATL54, a RING-H2 domain protein selected by a gene co-expression network analysis, is associated with secondary cell wall formation in Arabidopsis

Abstract

Biosynthesis of plant secondary cell walls is controlled by several master transcription factors. Ubiquitin ligases, which mediate ubiquitination of proteins, including transcription factors in the protein degradation pathway, are also believed to regulate secondary wall biosynthesis; however, the exact ubiquitin ligases involved in secondary wall formation have not yet been identified. We conducted a gene co-expression network analysis and found that ATL54, annotated as a RING-finger protein, was highly co-expressed with several transcription factor and enzyme genes involved in secondary wall formation. A recombinant ATL54 protein showed ubiquitin ligase activity. The expression of several biosynthetic genes of cellulose, lignin, and xylan in apical portions of inflorescence stems was up-regulated by ATL54 knock-out. The expression of Xylem Cysteine Peptidase1 (XCP1), which participates in the programmed cell death process of xylem tracheary elements, was down-regulated in middle stem portions of both ATL54-knock-out and ATL54-overexpressed mutants. Alteration of ATL54 expression levels did not, however, affect lignin and polysaccharide content and composition in whole mature stems. Our results suggest that ATL54 is an E3 ubiquitin ligase involved in secondary wall biosynthesis and programmed cell death during xylogenesis.

ATL54, a ubiquitin ligase gene related to secondary cell wall formation, is transcriptionally regulated by MYB46

“…Our previous study suggested that ATL54 may be involved in the regulation of programmed cell death as well as secondary wall formation during xylogenesis (Noda et al 2013). In this study, the tissue-level expression pattern analysis demonstrated that ATL54 was expressed in stem interfascicular fibers, xylary fibers, and vessels ( Figure 1A-D).…”

“…MYB46 is known to be a positive regulator of secondary wall biosynthesis (Ko et al 2009;Zhong et al 2007), while it was shown that overexpression of MYB46 did not activate XCP1 and XCP2, the genes related to programmed cell death during xylogenesis (Zhong et al 2007). In our previous study, we showed that the expression of secondary wall biosynthetic genes in apical stem portions was up-regulated by knock-out of ATL54 (Noda et al 2013), suggesting that ATL54 may act as a negative regulator of secondary wall biosynthesis. Spatially and temporally accurate lignin deposition and vessel element differentiation are known to be controlled by the action of both negative and positive regulators Zhao et al 2008;Zhao and Dixon 2011).…”

“…Spatially and temporally accurate lignin deposition and vessel element differentiation are known to be controlled by the action of both negative and positive regulators Zhao et al 2008;Zhao and Dixon 2011). Considering that ATL54 is a ubiquitin ligase (Noda et al 2013), ATL54 might cooperate with other positive regulators and contribute to optimization of secondary wall formation via degradation of transcription factors and/or other regulatory proteins involved in the process. The regulation of ATL54 expression during programmed cell death remains to be investigated.…”

“…A ubiquitination assay using a recombinant ATL54 protein showed that ATL54 had E3 ubiquitin ligase activity. The expression of secondary wall biosynthetic genes in apical stem portions of four-weekold plants was up-regulated by knock-out of ATL54, whereas the expression of Xylem Cysteine Peptidase1 (XCP1), a gene involved in programmed cell death in tracheary elements (Funk et al 2002), was downregulated in middle stem portions of both ATL54-overexpressed and ATL54-knock-out mutants (Noda et al 2013). However, it remains unclear how the expression of ATL54 is transcriptionally regulated.…”

“…In our previous study (Noda et al 2013), we searched the ATTED-II database (Obayashi et al 2009) for genes encoding RING finger family proteins that were coexpressed with secondary wall-associated transcription factor and enzyme genes, because RING finger proteins are the most frequent catalytic subunits of E3 ubiquitin ligases (Mazzucotelli et al 2006). As a result, we found that Arabidopsis Tóxicos en Levadura54 (ATL54, At1g72220) showed the highest correlation coefficients for several secondary wall-associated genes (Noda et al 2013). A ubiquitination assay using a recombinant ATL54 protein showed that ATL54 had E3 ubiquitin ligase activity.…”